##	from SigProfilerMatrixGenerator import install as genInstall
##	genInstall.install('GRCh37', rsync=False, bash=True)

vcf_path="/public/home/xxf2019/20220915_gastric_multiple/dna_combine/sigProfiler/vcf/vcf_all"
sigproextractor_out="/public/home/xxf2019/20220915_gastric_multiple/dna_combine/sigProfiler/extractor/all"

# from SigProfilerMatrixGenerator import install as genInstall
# genInstall.install('GRCh37', rsync=False, bash=True)

# from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
# matrices = matGen.SigProfilerMatrixGeneratorFunc("Lung", "GRCh37", vcf_path , plot=True, exome=False, 
# 	bed_file=None, chrom_based=False, tsb_stat=False, seqInfo=False, cushion=100)


## 默认会占满所有CPU，需要调整一下
from SigProfilerExtractor import sigpro as sig
sig.sigProfilerExtractor("vcf", sigproextractor_out , vcf_path , 
	reference_genome="GRCh37", opportunity_genome = "GRCh37" , cpu = 10 ,
	exome=True , minimum_signatures=1 , maximum_signatures=10)
